Comments (4)
The output format of Mothur's clusters is described on that page: http://www.mothur.org/wiki/List_file
from swarm.
Appears to be fairly trivial to convert swarm's output to a mothur compatible list file:
tr '\n' '\t' < test.swarms > test.swarms.list.tmp1
tr ' ' ',' < test.swarms.list.tmp1 > test.swarms.list.tmp2
echo -e "d1\t12345\t" | cat test.swarms.list.tmp2 > test.list
where d1 is my -d level, and 12345 is the number of produced OTUs. Tested with mothurs make.shared command, then ran a short analysis on the shared file.
from swarm.
Hi Adam,
indeed it is trivial. If I may, I suggest some modifications to avoid using intermediate files:
SWARMS="test.swarms"
OTUs=$(wc -l < "${SWARMS}")
(echo -ne "d1\t${OTUs}\t" ; tr "\n" "\t" < "${SWARMS}" | tr " " ",") > test.list
I also used the -n
option of echo to avoid the automatic \n
character. What do you think of that code block?
from swarm.
This feature is now implemented in the SWARM code. Option -r
or --mothur
will format the output file according to the mothur list file format.
from swarm.
Related Issues (20)
- Incorrect results with long sequences, very high gap penalties, and d>1 HOT 9
- Roadmap HOT 9
- table formats for making OTU table from swarm results HOT 2
- documentation: maximal input sequence length HOT 9
- Link to new swarm 3 paper HOT 3
- way too many clusters? HOT 7
- Issues with plotting: OTU not found HOT 3
- OTU table without abundance values HOT 6
- Compiling fails on Windows HOT 3
- maximal header length HOT 1
- uc file question HOT 7
- Invalid numeric argument for option -t or --threads HOT 8
- integer division might be one byte too small in some cases HOT 14
- Seeds not in same order as clusters in output files HOT 2
- Option to exclude seeds or clusters with low abundance HOT 1
- risk of silent 8-bit unsigned integer overflow in score matrix HOT 5
- fastidious boundary applies to the consolidated cluster mass? HOT 1
- Option to output cluster member ids/sequence id? HOT 3
- swarm terminates if any sequence in the input fasta file has an N HOT 2
- Refactor Bloom filter code
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from swarm.